Bottom Line:
Lucilia cuprina is a parasitic fly of major economic importance worldwide.Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina.Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance.

Affiliation: Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.

ABSTRACTLucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.

f1: Orthology comparison among Lucilia cuprina, Drosophila melanogaster, Glossina morsitans and Musca domestica.A total of 4,106 genes are SCOs that are shared among the four fly species; 12,160 L. cuprina genes are shared with at least one other species of dipteran. In this comparison, 2,062 genes (14.2%) are unique to L. cuprina.

Mentions:
We predicted 14,554 coding genes using de novo and homology-based predictions, of which 10,121 were supported by mapping RNA-seq reads (n ≥5) derived from larval stages (mixed) and adults (both sexes) of L. cuprina. Mean gene, exon and intron lengths were 12,197, 432 and 2,560 bp, respectively, with an average of 4.5 exons per gene (Table 1), similar to the findings for the genomes of D. melanogaster, G. morsitans and M. domestica101112. A total of 4,106 genes are single-copy orthologues (SCOs) shared among the four fly species, and 12,160 genes are shared with at least one other species of Diptera (Fig. 1). In contrast, 2,062 genes (14.2%) are unique to L. cuprina, with no homologues detected in any other dipteran for which genome sequence data are currently available (Fig. 1). Of the entire L. cuprina gene set, 9,822 genes (67.5%) have an orthologue (E-value cutoff ≤10−5) linked to one or more of 254 known biological (KEGG) pathways, most of which mapped to those in D. melanogaster (see Supplementary Data 3). The completeness of the genome is further supported by the CEGMA results (Supplementary Data 1). By inference, the majority of the L. cuprina gene set is represented in the present genomic assembly, and supported by extensive transcriptomic and inferred proteomic data (n=10,121 and 11,553 molecules, respectively) from multiple public databases.

f1: Orthology comparison among Lucilia cuprina, Drosophila melanogaster, Glossina morsitans and Musca domestica.A total of 4,106 genes are SCOs that are shared among the four fly species; 12,160 L. cuprina genes are shared with at least one other species of dipteran. In this comparison, 2,062 genes (14.2%) are unique to L. cuprina.

Mentions:
We predicted 14,554 coding genes using de novo and homology-based predictions, of which 10,121 were supported by mapping RNA-seq reads (n ≥5) derived from larval stages (mixed) and adults (both sexes) of L. cuprina. Mean gene, exon and intron lengths were 12,197, 432 and 2,560 bp, respectively, with an average of 4.5 exons per gene (Table 1), similar to the findings for the genomes of D. melanogaster, G. morsitans and M. domestica101112. A total of 4,106 genes are single-copy orthologues (SCOs) shared among the four fly species, and 12,160 genes are shared with at least one other species of Diptera (Fig. 1). In contrast, 2,062 genes (14.2%) are unique to L. cuprina, with no homologues detected in any other dipteran for which genome sequence data are currently available (Fig. 1). Of the entire L. cuprina gene set, 9,822 genes (67.5%) have an orthologue (E-value cutoff ≤10−5) linked to one or more of 254 known biological (KEGG) pathways, most of which mapped to those in D. melanogaster (see Supplementary Data 3). The completeness of the genome is further supported by the CEGMA results (Supplementary Data 1). By inference, the majority of the L. cuprina gene set is represented in the present genomic assembly, and supported by extensive transcriptomic and inferred proteomic data (n=10,121 and 11,553 molecules, respectively) from multiple public databases.

Bottom Line:
Lucilia cuprina is a parasitic fly of major economic importance worldwide.Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina.Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance.

Affiliation:
Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.

ABSTRACTLucilia cuprina is a parasitic fly of major economic importance worldwide. Larvae of this fly invade their animal host, feed on tissues and excretions and progressively cause severe skin disease (myiasis). Here we report the sequence and annotation of the 458-megabase draft genome of Lucilia cuprina. Analyses of this genome and the 14,544 predicted protein-encoding genes provide unique insights into the fly's molecular biology, interactions with the host animal and insecticide resistance. These insights have broad implications for designing new methods for the prevention and control of myiasis.